Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1999-05-21
2001-03-06
Yucel, Remy (Department: 1635)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S069100, C435S091100, C435S254100, C435S254110, C435S254200, C435S254210, C536S023100, C536S023700, C536S023740, C536S024300
Reexamination Certificate
active
06197517
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates to genes in
Saccharomyces cerevisiae
which are essential for germination and proliferation of
S. cerevisiae
and using the identified genes or their encoded proteins as targets for highly specific antifungal agents, insecticides, herbicides and anti-proliferation drugs. Specifically, the present invention relates to essential genes YFR003C, YGR277C, YGR278W, YKR071C, YKR079C, and YKR083C. The present invention provides antisense molecules and ribozymes comprising sequences complementary to the sequences of mRNAs of essential genes that function to inhibit the essential genes. The present invention also provides neutralizing antibodies to proteins encoded by essential genes that bind to and inactivate the essential gene products.
BACKGROUND OF THE INVENTION
Fungal pathogens are responsible for a large number of diseases in humans, animals and plants. Fungal diseases often occur as opportunistic infections in humans who have a suppressed immune system, such as in patients with AIDS, leukemia, or diabetes mellitus, or in patients receiving immunosuppressive drugs or chemotherapy. Fungal infections are a significant problem in veterinary medicine as well, and fungal diseases also affect plant crops which are critical to the agricultural industry. Since fungi are eukaryotic cells, many metabolic pathways and genes of fungi are similar to those of mammalian and/or plant cells. Therefore, treatment of fungal diseases is frequently hindered because antifungal agents are often toxic to mammalian or plant cells.
The most widely used class of antifungal compounds in human medicine is the family of azole compounds, which are used to treat both systemic and topical fungal infections. The common target of all azole compounds is the cytochrome P450 lanosterol 14&agr;-demethylase. Lanosterol demethylase is an essential gene required for the intracellular biosynthesis of sterols, which are critical components of biological membranes. In
S. cerevisiae,
the ERG11 gene encodes lanosterol demethylase. Although azole compounds are effective antifungal inhibitors, the enzymes involved in sterol biosynthesis are highly conserved in all eukaryotic cells. Lanosterol demethylases from all eukaryotic cells, including human, exhibit a high degree of nucleotide sequence identity, as shown in FIG.
9
. Thus, the azoles inhibit lanosterol demethylase from the host cell as well as lanosterol demethylase from yeast, which causes undesirable side effects upon administration. These side effects may be especially deleterious in patients who are already immunocompromised because it may make them more susceptible to other opportunistic infections. Therefore, the identification of new targets for new antifungal compounds with fewer side effects is an active area of clinical research.
The use of herbicides and insecticides are critical in agriculture to ensure an adequate food supply for a growing world population. One problem with current herbicides and insecticides is that agricultural pests often become resistant to them. Another problem is that many pesticides currently in use are highly toxic to farmworkers working in the fields, humans or animals who eat the food produced by the treated crops, or other plant and animal species that come in contact with the pesticide through soil, water or air contamination. Thus, new herbicides and insecticides that are less toxic to humans and animals and that are effective against resistant species of weeds and insects are desirable.
Drugs to prevent proliferation are critical in the treatment of diseases characterized by uncontrolled or poorly controlled cell proliferation. For instance, anti-proliferation drugs are used to treat many types of cancer, benign tumors, psoriasis, and to prevent restenosis after angioplasty. Identifying new targets for anti-proliferation drugs is an active area of research because different cells, especially malignant cells, vary dramatically in their responses to particular anti-proliferation drugs. It is often the case that an anti-proliferation drug will inhibit cell proliferation in one cell type but be ineffective in another cell type. Thus, the identification of new anti-proliferation drugs, directed against novel targets, provides a larger arsenal from which a physician can treat a patient with a cell proliferation disorder.
As discussed above, identifying new targets and compounds for antifungal drugs, herbicides, insecticides and anti-proliferation agents is critical for improvements in agriculture and in veterinary and human health. One promising avenue for identifying targets and compounds is the information contained within the complete genomic sequence of baker's yeast,
Saccharomyces cerevisiae. S. cerevisiae
has long been used as a model for eukaryotic cells.
S. cerevisiae
shares many basic cellular functions with other eukaryotic cells, including vertebrate, insect and plant cells. Furthermore, it is easy to grow
S. cerevisiae
and to manipulate its genes. Many of the genes of
S. cerevisiae
are specific to
S. cerevisiae
or to fungi in general, and have no homologs in other eukaryotic organisms. However, many genes from
S. cerevisiae
exhibit significant homology to genes in other organisms, including mammals, plants and insects.
The sequencing of the
S. cerevisiae
genome marked the first complete, ordered set of genes from a eukaryotic organism. The sequencing of
S. cerevisiae
revealed the presence of over 6,000 genes on 16 chromosomes (Mewes et al. (1997)
Nature
387:7-65; Goffeau et al. (1996)
Science
274:546-67). The sequence of the roughly 6,000 ORFs in the yeast genome is compiled in the Saccharomyces Genome Database (SGD). The SGD provides Internet access to the complete genomic sequence of
S. cerevisiae,
ORFs, and the putative polypeptides encoded by these ORFs. The SGD can be accessed via the World Wide Web. A gazetteer and genetic and physical maps of
S. cerevisiae
is found in Mewes et al., 1997. References therein also contain the sequence of each chromosome of
S. cerevisiae.
Approximately half of the putative proteins encoded by the open reading frames (ORF) identified in the sequencing of the yeast genome have no known function. The function of many others is assigned only by structural similarity to homologous proteins in other cell types. Thus, the role of many genes in
S. cerevisiae
is unknown. However, in order to use the information gathered from the sequencing of
S. cerevisiae
most efficiently for identifying targets or compounds for antifungal and anti-proliferation drugs, as well as herbicides and insecticides, the function of the many
S. cerevisiae
genes must be identified.
Citation of a reference herein shall not be construed as indicating that such reference is prior art to the present invention.
SUMMARY OF THE INVENTION
This invention provides genes in
S. cerevisiae,
a budding yeast, which are essential for germination or proliferation. The essential genes are useful as targets for new antifungal agents, insecticides, herbicides and anti-proliferation drugs. Specifically, the invention provides yeast essential genes YFR003C, YGR277C, YGR278W, YKR071C, YKR079C, and YKR083C.
The invention provides a method of comparing the sequences of the essential
S. cerevisiae
genes to sequences from plants, insects and vertebrates, including humans and non-human mammals, to determine whether the essential
S. cerevisiae
genes have any homologs in these higher eukaryotes. If no human or mammalian homologs exist, the
S. cerevisiae
genes themselves, or the proteins which these genes encode, provide targets for the design or discovery of highly specific antifungal agents for use in human patients or in veterinary settings. Similarly, if no plant homologs exist, the
S. cerevisiae
genes or their encoded proteins provide targets for the production of highly specific antifungal agents for plants. The advantage of the method is that the new antifungal agents would be expected to have few or no side effects in human or non-human ma
Pennie & Edmonds LLP
Rosetta Inpharmatics, Inc.
Shibuya Mark L.
Yucel Remy
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